Regulation of intestinal genes by CDX2 and other tissue-restricted transcription factors

CDX2 和其他组织限制性转录因子对肠道基因的调节

基本信息

批准号：
9537499
负责人：
Ramesh A Shivdasani
金额：
$ 38.22万
依托单位：
DANA-FARBER CANCER INST
依托单位国家：
美国
项目类别：
财政年份：
2010
资助国家：
美国
起止时间：
2010-09-01 至 2022-07-31
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/9537499
关键词：
Active Sites Address Adult Affect Barrett Esophagus Biochemical CDX2 gene Cells Chromatin Colorectal Cancer Data Set Dependence Deposition Development Digestive System Disorders Disease Distant Ectopic Expression Elements Embryo Endoderm Enhancers Enterocytes Epithelial Epithelium Functional disorder Funding Gastrointestinal tract structure Gene Expression Gene Expression Regulation Genes Genetic Genomics Goals Growth HNF4A gene Health Histones Hormonal Immunoprecipitation Inflammatory Bowel Diseases Intestinal Cancer Intestines Knowledge Life Maps Metabolic Molecular Mus Nucleic Acid Regulatory Sequences Organ Process Proliferating Property Proteins Regulation Regulator Genes Repression Role Site Specificity Stomach Technology Testing Time Tissues Transactivation Transcript Villus Wild Type Mouse crypt cell epigenome experimental study fetal gene complementation gene repression hepatic nuclear factor 1 improved in vivo innovation intestinal crypt intestinal epithelium mRNA Expression novel novel therapeutics progenitor recruit spatiotemporal transcription factor transcription factor CDX2

项目摘要

Project Description Common disorders of the digestive tract, such as Inflammatory Bowel Disease, colorectal cancer and Barrett's esophagus reflect profound epithelial dysfunction and gene dysregulation. Improved treatments require better understanding of the basis for intestine-specific gene control. Certain transcription factors (TFs) – CDX2, HNF4 and HNF1 – act at the distant enhancers of genes that define gut epithelial identity and function, but mechanisms of enhancer assembly, specificity, and activity are not well understood. Nor is it known how chromatin and TF dynamics in gut endoderm allow the emergence of distinctive digestive epithelia. This proposal addresses some of these fundamental questions in mouse intestinal cells in vivo. Among thousands of cis-elements that control intestinal genes, we identify a new class of tissue-specific enhancers that require CDX2 to exclude the repressive histone mark H3K27me3 from large genomic domains; H3K27me3 was not previously implicated at distant enhancers in adult tissues. These findings ascribe a novel, unexpected function for CDX2 at `anti-repressive' Type 1A enhancers that control the most quantitatively vulnerable genes in Cdx2-/- villus cells. Specific Aim 1 addresses the requirements and mechanisms of these novel enhancers. We propose genetic and biochemical experiments to test two central hypotheses: (a) that ~500 key intestinal loci are particularly susceptible to repression by virtue of extensive local deposition of H3K27me3, and (b) that CDX2 recruits the specific H3K27 demethylases KDM6A/B to oppose that locus-wide effect. We will use Eed-/- intestines, which lack methylated H3K27, to determine whether this feature is causally repressive and to attempt rescue of the genes most perturbed in Cdx2-/- intestines. Because Type 1A enhancers show a large difference in H3K27me3 levels between enterocyte progenitors in intestinal crypts and terminally mature enterocytes along the villi, we propose studies to test the hypothesis that this repressive mark limits high expression of enterocyte genes in replicating crypt cells. Specific Aim 2 considers the developmental origins and determinants of intestinal enhancers and asks why certain genomic domains acquire tissue-specific H3K27me3. This Aim builds on our discovery that nascent enhancers for all digestive epithelia are initially accessible throughout the early endoderm and that tissue-specific sites later strengthen in each organ while inappropriate enhancers are shut down. We will test the hypothesis that regions dependent on Type 1A enhancers in the adult intestine are the vestiges of enhancers that were used in development. We will also test the hypotheses that: (a) unless regional TFs reinforce open endodermal chromatin, enhancers shut down in a rostral-caudal wave, and (b) the state of chromatin at any time determines how the developing intestine responds to absence of CDX2. This proposal thus applies innovative state-of-the-art approaches to pursue exciting discoveries and address fundamental questions about intestinal gene regulation in vivo.

项目描述常见的消化道疾病，如炎症性肠病、结直肠癌和巴雷特食管反映了严重的上皮功能障碍和基因失调。需要更好地了解肠道特异性基因控制的基础。 (TF) – CDX2、HNF4 和 HNF1 – 作用于定义肠道上皮身份的基因的远程增强子和功能，但增强子组装、特异性和活性的机制尚不清楚。是否知道肠道内胚层中的染色质和 TF 动态如何导致独特的消化系统的出现？该提案解决了小鼠体内肠道细胞的一些基本问题。在控制肠道基因的数千个顺式元件中，我们发现了一类新的组织特异性需要 CDX2 从大基因组中排除抑制性组蛋白标记 H3K27me3 的增强子这些发现此前并未涉及成人组织中的远程增强子。将 CDX2 的一种新颖的、意想不到的功能归因于控制最多的“抗抑制”1A 型增强子具体目标 1 满足了 Cdx2-/- 绒毛细胞中易受攻击基因的定量分析的要求和要求。我们提出了遗传和生化实验来测试这两种新型增强剂的机制。中心假设：(a) ~500 个关键肠道位点特别容易受到抑制 H3K27me3 的广泛局部沉积，以及 (b) CDX2 招募特定的 H3K27 去甲基酶 KDM6A/B 可以对抗全基因座效应，我们将使用 Eed-/- 肠道（其甲基化 H3K27）来对抗这种全基因座效应。确定该特征是否具有因果抑制性，并尝试拯救最受干扰的基因因为 1A 型增强子之间的 H3K27me3 水平存在很大差异。肠隐窝中的肠细胞祖细胞和沿绒毛的终末成熟肠细胞，我们建议研究检验了这一假设，即这种抑制标记限制了肠上皮细胞基因的高表达具体目标 2 考虑肠道的发育起源和决定因素。增强子并询问为什么某些基因组结构域获得组织特异性 H3K27me3。我们发现所有消化上皮细胞的新生增强子最初都可以在整个早期获得内胚层和组织特异性位点随后在每个器官中得到强化，而不适当的增强子则被强化我们将检验成人肠道中依赖 1A 型增强子的区域的假设。是开发中使用的增强剂的痕迹。我们还将测试以下假设：(a) 除非区域转录因子增强开放的内胚层染色质，否则增强子会在头尾波中关闭， (b) 任何时候染色质的状态决定了发育中的肠道如何应对缺乏染色质的情况 CDX2 因此，该提案应用创新的最先进的方法来追求令人兴奋的发现和解决有关体内肠道基因调控的基本问题。